Unexpected Encounters
by cowgirlangel95
Summary: Team Bartowski is sent on a mission to stop previous Fulcrum and Ring agents from building another Intersect, while SHIELD is out to figure out why Hydra is importing a huge amount of data to once place. Both teams have something the other needs. Will they be able to find the missing information before they're taken out by the enemy, or worse, each other?
1. Chapter 1

_**A/N: Hello! It's been a while since I've dabbled in the Chuck and Agents of S.H.I.E.L.D. universes, and it feels good to return. Hopefully this time around all the characters won't be OOC…**_

 _ **Promo: /watch?v=TW135tIy2HE**_

 _ **Disclaimer: I don't own Chuck or Agents of S.H.I.E.L.D.**_

The original three of Team Bartowski was sitting in the center of Carmichael Industries, discussing the route that the former free-lance spy organization was going to take. Chuck and Sarah had spent the past two years rebuilding Carmichael Industries' resources in between Chuck still working at the Buy More and Sarah working through her recovery.

Casey let out an annoyed filled groan as he listened to the two Bartowskis sitting on the other side of the table from him as they explained the last part of putting the company back on the map.

"Now, now, Casey," Chuck began as he wrapped his hands around his coffee mug. He knew this would be Casey's reaction once he and Sarah presented the idea to him, and quite frankly, Chuck couldn't really blame him. It was a shift in the opposite direction Casey was used to, especially after working with Verbanski for a year. "We talked about this before a few years ago. Just because Carmichael Industries would be more on the cyber security side doesn't mean that there won't be some field ops –"

"No, but it implies it," he interrupted.

"So you'll have more time for target practice," Chuck reasoned. "That and you never know when someone like Shaw is going to pop back up. Something like that happens more often than you think," he explained; which it was true. However, Chuck knew that Casey wouldn't be in the field as much as he would want. _Maybe he could do some side work for the CIA; that is if Beckman's offer is still good despite it being two years old._ "Who knows, if there aren't that many assignments for you coming across the table, maybe you can work something out with Beckman."

Casey opened his mouth to respond, but the sound of Morgan's voice came from behind them. "And – it was your idea to come back after things with Verbanski didn't work out."

Sarah, Chuck, and Casey turned to see Morgan walking down the stairs into Castle, and all of them were giving the little bearded man the same look, plus a barely audible grunt coming from Casey.

He paused once he reached the last step and looked at them. "What? It's true – so what if Casey missed us?"

Chuck gave his best friend a disapproving glance as Sarah spoke. "Morgan, what are you doing down here?"

"Yeah," Chuck echoed. "I thought some big hot shots from corporate were going to be at the store this morning."

Morgan bobbed his head from side to side. "They're in the store right now, actually. But I'm letting Big Mike handle them," he explained as he walked over towards the table and sat down in one of the rolling chairs. "If they need me, Mike will let me know. So, how are the company plans coming along?" he asked as he picked up one of the open files near him and began to look at what was inside it. Casey quickly snatched it out of his hands, clearly startling Morgan as he jumped back and nearly toppled the chair he was sitting in over.

Before anyone could give him an answer, their main conference screen came to life and revealed an image of General Beckman.

"General," Casey greeted.

"Team," she returned.

"General, it's definitely great seeing you again," Chuck began, "but why are you calling?" he finished in a confused tone.

"If you would let me explain, Bartowski, I would do just that."

"Sorry," Chuck rushed in his usual manner.

"Now – recently a warehouse in Minsk has been under the CIA's and NSA's radar due to some suspicious activity," she began as she pressed a button on her keyboard, bringing up the image of the warehouse on a side monitor. "One of our undercover agents was surveilling the area when he spotted these two men entering the building." Beckman brought up their images on another one of the side monitors, and once Chuck laid his eyes upon them, their files came up before his eyes.

 _Christopher Eyre – Former Fulcrum software engineer – previously hired at Roark Industries – Head engineer on the Fulcrum Intersect Project –_ _Captured_ _ **Escaped**_

 _James Belle – Ring Software Engineer – Connections to Cybertech – Last known location: Paris, France, April 2010 – Built cypher_

Chuck blinked as he came out of the flash. "Wha… what are the Ring's and Fulcrum's previous heads of their software divisions doing there?"

"Once they were identified, we took an infrared image of the compound, and we found most of the warehouse walled with servers and –"

"—an Intersect White room, along with a lab to build the cypher," Chuck concluded.

Both Sarah and Casey's eyes widened. "But who would want to build an Intersect? Both organizations were dismantled long ago," Sarah reasoned.

"It doesn't matter who is building it, but the fact that it's out there. The reason I called you is because you… four," Beckman stammered as she eyed Morgan, "…are all of what's left of the Intersect project. I need you to retrieve what they have made this for and bring the warehouse down."

Casey and Sarah nodded their heads in agreement, but Chuck was the only one who spoke. "No."

"Bartowski, what are you trying to pull?" Casey muttered.

"Chuck, it's not safe out there if we let an Intersect fall into the wrong hands," Sarah explained.

He nodded. "I know, and that's exactly my point, Sarah. I know that if we retrieve their progress and hand it over, it's not just going to sit in some government vault forever. It won't be long before someone like Decker or Quinn comes along again to try and use it. My dad never wanted that. If anything gets retrieved, it's going somewhere I know anyone won't find it."

Beckman took her glasses off the bridge of her nose and folded them in front of her. "Agreed."

Chuck looked over at Sarah. "One more mission?"

A small smile came over her lips. "I thought we weren't supposed to say that," she lightly teased. "Yeah – one more mission."

Chuck returned Sarah's smile and then faced the screen again. "When do we leave, General?"

"A plane will arrive at the airport to take you to Minsk within the hour. Good luck," she said before she ended the feed.

Morgan stood up and clasped his hands together. "Alright! I'll start packing!"

OoOoO

"Morgan, how does the perimeter look?" Chuck asked over the com as he, Sarah, and Casey entered the warehouse.

"All good, there's a few baddies around the corner, but you should be in the next hall by the time they even move an inch," he explained as the sound of slurping filled the line.

The three team members stopped in their tracks. "Moron, are you drinking coffee?" Casey asked, now recalling how Morgan could be on missions.

"Give me a break Casey, it's cold out here!" Morgan defended.

Chuck shook his head as the three headed down the hall. "That's fine, Morgan, just mute your com when you do that, okay"

"Okay, got it."

The three of them continued down the hall. "Alright, Chuck," Sarah began. "Where to next?"

Chuck pulled back his sleeve and looked down at his father's old forearm computer. Over the years, Chuck had made some upgrades to it so it could keep up with the fast pace of modern technology. He tapped the screen a few times and led them down the next corridor.

After a few more minutes of weaving throughout different passageways, a loud crackling came over their coms. "Guys – think – there is someone –" they heard Morgan say before the coms went dead.

"Morgan?" Chuck asked as he tried to get him back on the line. "Morgan, are you there?"

Casey let out a grunt as he raised his gun in front of him. "Looks like we've got some company."

Sarah nodded her head in agreement. "Someone must have found out we were here. You two go find the Intersect white room, I'll patrol the area."

"No, Sarah," Chuck protested. "We should all stick together."

"She's right, Chuck," Casey countered. "We don't know how many they have, and the longer she can stall them, the more time you will have to get everything that is related to the Intersect."

"Why can't you go?"

"Walker is quicker when it comes to stealth."

Sarah took ahold of Chuck's hand. "Don't worry about it," she assured him. "I'll be fine." She leaned in and kissed him before she turned and headed down the hall. Sarah turned her head to face them one last time before they headed to find the white room. Before she headed around the corner, Sarah inhaled a calming breath and raised her pistol. She headed back the way they had come and checked each corner. Sarah approached the end of the hallway and was prepared to head around the corner when her gun was knocked out of her hand and she was met with a head of black hair.

 _ **A/N: Let me know what you thought! Not sure how often I'm going to be updating, but I hope to see you soon!**_


	2. Chapter 2

_**A/N: Wow, I didn't expect to get this much feedback considering it's a crossover. So thank you all! I'm hoping to try and update about once a month in the very least so I can focus more on college stuff. Quick timeline note about SHIELD, it's a brief AU. There are a few more days in between the time they saved Lincoln to the time he woke up.**_

Coulson walked into his office and approached May. "Anything on it yet?"

May shook her head as she looked at the tablet in her hands. "All we've been able to figure out for sure is that it's some sort of computer storage facility."

Coulson crossed his arms and sighed as he stood beside her and looked at the monitor. "And that's what you had figured out two hours ago."

"Mhm. The infrared scan didn't really help any matters at all like we had originally hoped," she said as she brought the image up on the monitor. "All it gives us is the layout."

Coulson raised an eyebrow as he stepped closer and tried to wrap his mind around what he was looking at. "What's with the large room in the center?" he asked.

"Unknown, other than it's one of two rooms. The other being some sort of storage, like a supply closet."

"Have we been able to intercept any sort of communications? Data transfers?"

May nodded as she tapped something on the tablet and brought up what they've been able to retrieve, all of which was gibberish to both of them. "Yes, but the only one here who could possibly give us any insight on it is –"

"I know," Coulson interrupted. After a long moment of silence and much deliberation, he said, "Bring the team in here. I'll go get her."

OoOoO

Both Simmons and Fitz watched as Skye stared absentmindedly at Lincoln, impatiently waiting for him to wake up. She had been like this for the past three hours, and nothing was going to tear her away from his side, not even food. Jemma had desperately tried to help Skye unwind a bit, she even brought some snacks over to her, but they sat untouched at the base of her chair.

"Do you think she'll be alright?" Jemma finally asked after a few minutes, imagining that Skye was experiencing something similar to when she herself was waiting for the man beside her to wake from his coma. To be honest, she couldn't really blame Skye for acting the way she was. It's hard to watch someone you really care about fight for their life.

Fitz nodded as he rubbed the back of his head. "Uh yeah. Yeah, she should be. I think once he wakes up she'll be fine. She's just worried, you know…" he babbled.

Jemma allowed a small smile to grace her lips as footsteps approached them. The two of them turned as one and saw Coulson nearing them. "Did she come out yet?" he asked as his eyes drifted over towards her.

"No, sir," Fitz responded.

Coulson simply nodded as he approached the containment area and sighed. He lightly tapped the glass with one of his knuckles to get her attention, and then beckoned for her to follow him. If he didn't know Skye any better, he would have missed the slight hesitation she made before she stood up and walked through the door.

"What is it?" she asked once she came face to face with him, but Coulson remained silent as he led her into his office. Once there, Skye looked around the room and saw Gonzales and May facing the view screen while Mack and Bobbi were over by the windows talking amongst themselves. Skye repeated her request, and it seemed that at the sound of her voice, the apparent spell that was in the room had broken and everyone turned to face her.

Coulson picked up the control from his desk and pressed one of its buttons. "A few hours ago, one of our feeds came across this," he began as the image began to zoom in. On the screen appeared a rather old warehouse with several trucks surrounding it. "We have reason to believe it is a Hydra facility, one of their older ones in Minsk from the Cold War that they decided to bring back up and running. We thought it might be some sort of weapons outpost. However, when we scanned the area to see what they were holding, we came up with this," he finished as he brought up the image overlay on the screen.

Skye slowly stepped up to the monitor and raised an eyebrow. "It looks like some sort of server station."

"Exactly what we thought. I want a three man op, me, May, and Skye, to go in and retrieve whatever they have there. Who knows, maybe whatever is there can get the upper hand to these guys."

Skye opened her mouth to respond, but Gonzales beat her to the punch. "I also want to be a part of this op. Otherwise, I will reject this mission approval."

Coulson gritted his teeth as he held back a harsh response. It didn't matter how many lives could be saved by this mission; all that mattered was that one of Gonzales' men was on the inside. "Fine," he reluctantly agreed, knowing that somehow this mission would be far too important to argue about logistics. "May, fire up one of the quinjets. We leave in ten."

Everyone nodded and filed out of the room, but Skye stayed behind. Once everyone had cleared out, she said, "Coulson, I –"

He held up a hand, knowing where she was going. "I know you want to stay here in case Lincoln wakes up, but I _need_ my best computer expert out there to retrieve everything we can. And with Gonzales going, I'm going to need more muscle just in case. Don't worry, Simmons can look after him and let you know of any progress."

Skye nodded her head in agreement. "Okay."

"Good. Here," he said as he picked up a tablet from his desk and handed it over to her. "Maybe you can try to figure out what it is on our way over there and how to get into their system. Once we retrieve all we can, I want that place leveled."

"Copy that," Skye replied as she took the tablet and headed out to the hangar.

OoOoO

As Skye was trying to decipher what was in front of her, Coulson approached her and sat down beside her. "Any progress?"

Skye bobbed her head back and forth. "Sort of," she replied as she tapped on something. She had been working on this for the past three hours and she had yet to understand a lot of it, and it frustrated her to no end. "All I've been able to find out is that the corridors surrounding that large room are lined with servers, and all of them are wired into the same room. The amount of data storage that they have in here is incredible."

"How much?"

Her eyes widened as she shook her head. "I'm not exactly sure… possibly a zettabyte, maybe more."

"Do you think it's for some sort of weapon?"

"Again, I'm not exactly sure," she said as she brought up another screen. "What kind of computer would need this much data space? Not even Zola's algorithm needed half of this. So what on Earth could they be building? From the communiques and what I can decipher out of the tech lingo, the only thing I could guess would be they're trying to build some sort of super computer. However, what would it be for? It would be stupid to keep all that data in one place; Hydra is too smart for that."

Coulson raised an eyebrow. "What couldn't you make out?" he asked, knowing that there wasn't much that Skye couldn't find out somehow.

"There was one main one that was repeated several times. They called it a cypher."

Coulson nodded as he stood back up. "Hopefully we'll get some answers once we get there."

OoOoO

Once May set down the quinjet in a field not far from the warehouse, Coulson started to go over the plan. "Our task is simple – get in, get as much intel as we can before they discover we're there, and then blow the place. Skye, is that jamming signal ready?"

Skye nodded as she continued to type away on her laptop. "Almost – once I start the program, the rotating jamming signal will activate ten minutes after, leaving plenty of time for us to get on the premise before Hydra knows we're there."

Gonzales let a low groan escape his lips. "And if this is a trap, we're all dead. That thing they're building could be some sort of advanced infrared scanner."

Skye shook her head as she continued to type. "That's highly unlikely. They don't have the tech there to build something like that – they don't even have the materials to build any sort of pulsar weapon. We found that out way before we left. They could be trying to program the software for any one of those, but it wouldn't make sense to have all of that storage for one weapon, let alone away from any physical prototype. What they're most likely building is a super computer – and any sort of computer can be taken care of easily, as long as all components are blown to bits."

The older man rolled his eyes at Skye's words. "But you're still not sure what it is exactly. Going in with _this_ many unknowns is still a huge risk," he growled. "If you had actually _told_ me the full specs of your plan before we left the base, I never would have sanctioned this mission."

Coulson approached Gonzales and stopped just as their noses were about to touch. "Going in with many unknowns is part of the job – it's what SHIELD does. It's what we've done for years, and if you don't like that, you can stay here," he threatened. When Coulson was met with silence from the other man, he continued on without taking his eyes off of him, "Skye, the hard drive?"

She lightly tapped her leg. "In my pocket."

Coulson nodded as he put a magazine in his gun and checked it. "Alright – let's move out," he finished just as Skye hit the enter key, sending the jamming signal into its countdown. The four SHIELD agents headed down the ramp of the quinjet and carefully made their way towards the compound. Once they crossed the pavement, the team slipped into one of the doors that was left propped open. "Time?" Coulson asked.

Skye looked down at her timer. "Three seconds," she replied.

"Okay, now we head for the center room – Skye on point, May you cover behind us –"

"Coulson," Gonzales interrupted, "do you really think it wise to have…" he paused, making sure to choose his words carefully, " _her_ leading us?" he asked, his voice filled with bitterness.

Coulson rolled his eyes. "Considering she is the one that knows the layout best, is going to need to get to their tech as quickly as possible, and she can level a room if need be faster than any of us can."

" _That's_ what I mean!" Gonzales hissed through gritted teeth.

"Just because she has powers doesn't mean –" he started, but froze when he saw May raise her fist out of the corner of his eye, signaling them to stop.

Everyone paused and heard the soft echoes of voices coming from somewhere nearby. "May – you take care of them, the rest of us will head to the main room," Coulson ordered.

May nodded as the other three agents headed down the hallway, and then she headed in the general direction that the voices were coming from. By now, they had stopped, but as May moved closer to the joining hallway, she noticed a shadow slowly approaching the corner. She stopped just shy of the corner and waited until the tip of her opponent's gun came into her line of sight. May knocked the gun out of her enemy's hands – a tall blonde woman – and blocked the woman's counter strike. As the two continued to fight, they moved down the hallway the blonde had just come from. Eventually, May was able to throw her up against the wall, but before May could do anything else, the other woman was back on her feet and sent May tumbling down the hallway thanks to an elbow to her face and a kick to the stomach. The other woman reached into her boot for another weapon, but May swept her leg, causing the small gun she was reaching for scattering down the hallway. Both of them headed for the weapons and continued to try and outdo the other – leading them closer and closer to the center room.

 _ **A/N: If you could let me know what you thought of it/ liked/ disliked before you leave it would be much appreciated. See you next time!**_


	3. Chapter 3

_**A/N: Dang… time sure flies. College can sure keep one busy! Anyway, thank you to all of you that have favorited, followed, and reviewed!**_

After rounding the final corner, the door leading to the Intersect white room came into both Casey's and Chuck's line of sight, standing a few yards away from them. "That's it, Casey," Chuck announced as the two of them continued to approach, "all we have to do is get through the security system and then upload it to the server at Castle."

"How long is that going to take?"

"Only a couple of minutes longer than it does to upload it to the glasses. Maybe sooner since technology has improved since we last had to deal with this. As long as Sarah continues to patrol the perimeter, we shouldn't get –" he tried to explain, but he was interrupted by the sound of several handguns being cocked. "– caught…" Chuck trailed as he looked at the forearm computer. "They weren't there a few minutes ago."

Casey shook his head as he raised his own pistol towards the three agents aiming at both himself and Chuck in front of them. No matter how much Chuck grew over the past few years, sometimes he could still be his old self. "Shut up, Chuck!"

"Maybe I need to figure out how to widen its radius…" he continued to ramble as he began pressing different buttons on it.

"Chuck…" Casey growled.

"Sorry."

One of the three member team, he was older than the other two and put most of his weight on a cane, tightened his grip on his gun. "Hands up! Both of you! Now!" he barked.

The threat alone made Casey want to laugh. Someone who he could take down with one hand was making that type of threat to him. Casey didn't know whether or not to take it as an insult or a joke. "I don't think so."

"Lower your weapons now and step away from the door," the man continued.

"Funny…" Casey trailed. "I was going to say the same thing to all three of you."

The older man turned to the other man of the group. "Somehow they were able to figure out we were here despite all of our security measures, Coulson. You're lucky we caught them before they uploaded it to their new location and abandoned this warehouse."

As the man continued to talk, Chuck looked at the other members of the group, and immediately felt massive amounts of data being sent to the front of his vision.

 _Gonzales, Robert. Former member of S.H.I.E.L.D. Attempting to head new organization of S.H.I.E.L.D._

 _Coulson, Phillip. Former member of S.H.I.E.L.D._ _Killed in the Battle of New York_ _. Current assignment: unknown. Last known ware bouts: unknown._

 _Skye. Former Rising Tide member. Former member of S.H.I.E.L.D. WARNING - Skilled hacker. Current assignment: unknown. Last known ware bouts: unknown._

As Chuck came out of the flash, he turns to Casey. "Casey, they're not part of Fulcrum or the Ring, they're former S.H.I.E.L.D. agents, Gonzales, Coulson, and Skye. They're our –"

"How does he know that?" Gonzales growled as he now aimed his pistol at Chuck, causing him to raise his hands out of fear.

"Gonzales," Coulson warned, "stand down!"

Gonzales shook his head. "He's clairvoyant, how else would he know that information about us. They have powered people working for them, and we need to shoot while we have the chance before he can warn all of his buddies."

Chuck looked over at Casey's hand, and could tell that if Gonzales said one more word that Casey would fire. While his most 'recent' training told him not to do what just came to his mind, he knew that it would be sure death if he didn't revert back to his old tactics for just a moment. "Casey, don't shoot; they're our allies! They're all former members of S.H.I.E.L.D."

Without taking his eye off of Gonzales, Casey said, "S.H.I.E.L.D. is gone, Chuck. It was found that most of the organization was Hydra."

"Not everyone was."

"I don't care if they are our allies because they aren't acting like it at the moment," Casey replied. "They pull the trigger, the NSA, the CIA, and Sarah are not going to be happy," he finished, trying to mutter it so only Chuck's ears could hear, but the other man lowered his weapon upon hearing what Casey had said.

"You're part of the CIA and the NSA?" Coulson asked.

Chuck grimaced slightly as he and Casey made eye contact. "Yeah, more or less, yeah."

Casey shook his head ever so slightly as he returned his focus to the other three. _The more things change, the more they stay the same._

"That could explain how they would know if they were working with Agent 13," Skye suggested.

Gonzales shook his head, still not buying anything. "But he knew certain information that no one should."

Coulson signaled for both Gonzales and Skye to lower their weapons. Skye complied, but Gonzales was not all that eager at complying just yet. "Why would they send agents on an op to a Hydra base?"

At the mere mention that this was, in fact, a Hydra base, Chuck's face paled while Casey's eyes only widened slightly. "Casey, if former techs from both Fulcrum and the Ring are working for Hydra, that means…" he trailed.

"Yeah, I know what it means."

Coulson raised an eyebrow at the sound of the two organizations. "Fulcrum? The Ring?" he asked.

"They were terrorist organizations from years ago," Skye explained. "The Rising Tide were trying to combat them when I first joined."

"So what is it exactly that they're trying to build here?" Coulson though aloud.

Casey shook his head, knowing that Chuck may give them far too much information than they would need. "Chuck, no."

"Casey, if they're going to be helping us, then they're going to know something on it. They don't need to know everything," he explained. After being greeted by silence, Chuck continued. "They're trying to build the perfect soldier or spy."

Skye shook his head. "With no training rooms? No labs? Only computer servers? That doesn't make any sense. Besides, they tried that with Centipede, succeeded, but that specific program was brought down."

"It's not that kind of super soldier," Chuck retorted. His stomach started to churn as he thought of the possible outcomes of what could have been accomplished with Intersect technology in Hydra's hands.

"Then what exactly are they trying to do?" Coulson asked.

Chuck let out an angered sigh as he tried to bring himself to answer the question. His father knew something like this would happen if the Intersect got into the wrong hands, and now it was in the hands of an organization that was more powerful than Fulcrum and the Ring combined. "It's a supercomputer. One capable of turning any ordinary person into the perfect secret agent."

All three S.H.I.E.L.D. agents looked at each other, trying to grasp this sort of concept. But before anyone else can say anything, one of the doors leading to this part of the warehouse crashed open, and both May and Sarah come tumbling through it; both of them ready to finish the other one off.


	4. Chapter 4

_**A/N: Hey all! I was hoping to get this up sooner, but I had quite a bit happening lately. Anyway, here it is. Enjoy :)**_

The metal door came swinging off its hinges at lightning speed as both Sarah and May came crashing through it and rolled onto the floor. Both agents got to their knees, and then hopped to their feet, prepared to finish the other off as they set back into their fight stances. However, neither of them were able to deliver any sort of blow before the urgent pleas of Chuck, Coulson, and Skye filled the room.

"May, wait!"

"Sarah, no!"

"Stand down, Melinda!"

Sarah and May shifted their focus to the group. Both Chuck and Skye had their arms extended as if they were going to rush in and pull the two apart at any moment. That is, Chuck looked as if he were about to leap in between the two at any moment while Skye seemed to be prepared to intervene if necessary. The two of them returned their focus to each other and slowly lowered their arms and slowly backed their way towards their teams.

"Chuck, what is going on?" Sarah asked as she wiped a small trickle of blood from her nose.

"It's alright, they're S.H.I.E.L.D.; they're on our side."

"S.H.I.E.L.D.? I thought they were dismantled a while ago. Besides, why would S.H.I.E.L.D. be on a mission specifically for the CIA and NSA?"

May raised an eyebrow as she overheard what Sarah had said. "Why is a CIA/ NSA team here?"

Chuck let out a sigh as he rubbed the back of his neck and then looked at his watch. _We're wasting so much time!_ his mind thought as he anxiously looked at his watch. "Let's briefly recap. As I was saying… we were informed that former Fulcrum and Ring agents were here building what's in these rooms," Chuck said as he pointed to the two doors on his left, "a type of super computer. We were sent to retrieve what they had made so far, all files on it, and then blow the base. It appears that the agents we are after are now a part of Hydra, and trying to make the computer for them. The computer they're trying to build is too dangerous to be in the wrong hands."

"What kind of supercomputer is it?" Skye asked. "You said it can turn basically anyone into a super spy. Can you give us any more information on what else it can do or how it can do it? What you've said so far is rather vague."

Chuck pressed his lips into a thin line. "I'm afraid I can't say – classified. I've probably told you too much as it is," he explained, which earned a confirming grunt from Casey. Chuck had to keep from rolling his eyes, but he couldn't blame Casey. In fact, he knew that he had said too much, but when has he not? It may have been a while since he has on a mission, but he was pretty much the same guy that Bryce sent the first Intersect to all those years ago. Beckman could probably throw the book at him, again, but right now it didn't matter. What mattered now was making sure that the Intersect didn't fall into anyone else's hands. And that included the S.H.I.E.L.D. agents standing in front of him. If that meant giving them some information on it, then so be it. Besides, what could they do with what he had told them? Not much, that was for sure. All that they could possibly conclude would be speculation.

"Now," Gonzales began, "can you tell us how _he_ knew who we are?" he asked as he pointed his cane towards Chuck. "Is this supercomputer that they're building related to how he knows?"

"Classified," Sarah replied flatly. "Now that we know we're all allies… for the most part, we need to bypass the security system and get through those doors."

Everyone in the room agreed as both Chuck and Skye approached the door. Both of them gave each other a skeptical look, doubting the other's skill.

"You know," Skye began, "I think the best should tackle this project."

Chuck smirked at her comment. "I couldn't agree more."

Casey rolled his eyes as the two techies continued to argue over who should open the door. "Are we seriously doing this right now? Don't we have better things to be doing?"

"Look, I was the best the Rising Tide ever had. The only hacker who could beat me was the Piranha," she explained as a small, cocky smile spread over her lips. She knew she had him.

Or so she thought.

Chuck returned to her a smile of his own. "How ya doin'?" he asked as he pulled his toolkit out of his pocket and started to work at the door's security.

Skye's face fell as Chuck passed her. She couldn't believe what she had just heard. Piranha was someone that she always wanted to meet. Both skill wise and efficiency wise, Piranha was superior. It made her a bit jealous. She knew that he had been hacking far longer than she has, but no matter what she did, she just couldn't get the upper hand on him, even when he was on hiatus. After a moment, Skye turned and approached Chuck's side. "You… you turned down an invite to join the Rising Tide! Probably one of the few to ever do that."

Chuck shrugged as the locks to both of the doors clicked. "Yeah, well… the CIA kind of frowns upon joining those sort of organizations. Even if they had reached out to me in college when my hacking days were more in their prime, I still probably would have said no. Not one for that kind of hacking," he explained. "Alright, Casey, Coulson, you head into the storage room over there and collect any of the files they have on… it," Chuck ordered, nearly letting 'the Intersect' slip. As the two men headed towards the other room, May followed them. "Okay then," he muttered, "everyone else is with me."


	5. Chapter 5

_**A/N: Hey all! So sorry for the long time in between chapters. My final semester is kicking my butt right now time wise. Hope this was worth the long wait!**_

With their guns drawn, Casey opened the door to the intel room and he, Coulson, and May headed inside. All three of them scouted the room – behind every filling cabinet and in every corner. Once they made sure no one else was in the room, they lowered their weapons and looked about the room.

"What is it we need to look for?" May asked as she turned to face the two men.

Casey removed the pack from his back and made his way over to the shelves. "You two look through those filing cabinets over there. Collect anything that has the words 'Intersect', 'cypher', or analysis reports on them themselves," he explained as he started shoving what appeared to be hard drives and other electronic components into the smaller pocket of his bag.

"What about any intel that they have on us, specifically?" Coulson wondered. "Shouldn't we grab some of that, too? I know we're blowing this base sky high so they won't have this for much longer, but shouldn't we try and take whatever we have?"

The ex-Marine shook his head. "That won't be necessary. If Chuck and Sarah succeed on their part all that info will be recovered, and that stuff will be kindling."

May and Coulson exchanged a look before opening the filing cabinets and beginning their search. As the two of them started searching through files, Coulson's mind began to race. _Why on earth would we not need to recover their intel? A computer that transforms someone into a superspy? Not needing to recover the intelligence? Do they both-_

"Got it," May said as she pulled a large white three ringed binder from the filing cabinet. "Information on the Intersect, the cypher, and all its testing," she continued as she pulled another binder out from the drawer.

Both Coulson and Casey approach May and Casey grabs the binders from May. "Perfect," he said as he stuffed them into the bag. "Now to get out of here," he added, just before the clicking sound of guns cocking reached all of their ears.

"That can't be good…" Coulson muttered.

"Drop your weapons and turn around with your hands up!" someone yelled from behind them.

Doing as they were told, they dropped their weapons in front of them and turned to face the Hydra team in the doorway.

One of them let out a humorless laugh as he stepped towards them, his dark eyes matching his personality. "Well, well, well… if it isn't Colonel Casey. Doesn't this seem familiar," he mocked as he stopped mere inches from his face. He looked at the bag Casey was still holding in his hand. "Bet I know what's in here," he continued as he grabbed the bag from Casey's hands and let it drop to his feet.

Casey narrowed his eyes. "Miles," he growled. Before he could do anything else, a voice came over the head of the Hydra team's radio.

"Sir, we have the rest of them in the White Room."

Mile's smile grew as he reached for his radio. "We shall be there momentarily," he responded. He reached for his gun, and then gestured towards the door with the barrel. "After you."

* * *

Sarah, Chuck, Skye, and Gonzales all filed through the other door. Skye raised an eyebrow as she eyed the room. It was covered in white tiles, and the only other thing in there besides themselves was a computer console sitting on a stand on the middle of the room.

As Chuck and Sarah made their way to the pedestal, Skye asked the open air, "What on earth is this room?" Skye wasn't expecting an answer. If anything she was wondering aloud as she looked at the white paneling stretched throughout the room.

Neither Chuck or Sarah bothered to answer – they just merely knelt down by the pedestal as Chuck pulled out his tools.

"What is this room used for?" Gonzales echoed, putting a little bit more force behind his words. Again, Chuck and Sarah remained focused on their task. "Leadership should operate with transparency! Tell us, or –"

"Or what?" Chuck interrupted as he turned to face the two S.H.I.E.L.D. agents. "You'll shoot us? Because that always works," he deadpanned, clearly annoyed at the older agent. "Believe me when I say that you know too much as it is, and that you don't want to know what this thing can do. It's dangerous and it needs to be rid of… once and for all."

Skye approached the group. "Is there anything we can do to help?"

Sarah let out a sigh as Chuck started to punch commands into the console. "Just cover us for now."

Slowly, the device used to install the cypher rose up, revealing the small brain of the Intersect. With a gloved hand, Chuck carefully took it out of its place, placed it inside of a bag, placed that into a case, and slipped it into his bag.

"Look," Gonzales pushed as he leaned on his cane, "if this thing is so dangerous then why are we just letting you take it? Clearly you haven't been doing your jobs if this keeps on popping up, so it should be placed in secure hands," he growled.

"Gonzales!" Skye yelled.

"Hey!" Sarah stepped in. "We can argue about this later. Right now we need to get –" she started, but was cut off when a strike team entered the room, weapons drawn.

"-out…"

"Hands up, all of you!" one of them yelled.

All of them complied while Sarah, Chuck, and Skye rolled their eyes.

"Or I could…" Skye whispered, but Gonzales cut her off.

"Shut it, Skye. We don't need to unleash _that_."

One of the agents reached up to his radio. "Sir, we have the rest of them in the White Room," he said.

"They have Casey and the others," Sarah whispered to Chuck.

"We shall be there momentarily," a man over the radio said.

Both Chuck and Sarah looked at each other in shock as the recognized the man's voice. "Miles," Chuck breathed. After Chuck uploaded the Intersect 2.0, they tied up the group that attacked them and called a CIA team to arrest them.

"There must have been other Ring agents in the vicinity," Sarah muttered back.

"Which would make sense seeing how they nearly took over the CIA and the NSA a year later," Chuck concluded.

Moments later, Casey, May, and Coulson came through the door followed by Miles and his team. "Well, well, well… look like we have the entire Team together once again," Miles taunted, "plus a few extras," he added as he eyed the S.H.I.E.L.D. agents. "Don't count on the Intersect to save you this time." After looking over the group for a while, Miles ordered, "Kill them all, then prepare the Intersect for uploading."

 _ **A/N: Bit of a cliffhanger, but I needed to cut it off there :) Two to three chapters left. Until next time!**_


	6. Chapter 6

_**A/N: I'm so sorry it took me so long to get this chapter up! Life has been rather busy and frustrating. Sadly, it is the last chapter, so I hope I did it justice. Enjoy!**_

"Well, well, well… looks like we have the entire Team together once again," Miles taunted, "plus a few extras," he added as he eyed the S.H.I.E.L.D. agents. "Don't count on the Intersect to save you this time." After looking over the group for a while, Miles ordered, "Kill them all, then prepare the Intersect for uploading."

Before the men could place their fingers on the triggers of their guns, the ground began to tremble beneath them. The Hydra team, along with Chuck, Sarah, and Casey, began to look around while confusion plastered their faces.

"What is this?" Miles questioned, gun still aimed at the group of agents in front of him. "What's causing this?"

While they were still trying to perceive what was going on, a small smile graced Skye's lips as she lowered her arms, extended one of them towards the Hydra agents, and sent a compact wave of air towards them, throwing them all backwards into the wall – knocking them unconscious before slumping to the ground.

The rest of the group lowered their hands as the three former CIA agents looked at Skye bemused. "Wha… what? That was you?" Chuck managed to stutter out.

Skye nodded as she reached down for the pistol she had dropped earlier. "Yeah. Not exactly something I'm happy about having at the moment but, you know… life can be rather complicated."

"I thought I told you _not_ to do that?!" Gonzales growled.

"We can argue about that later," Coulson cut in as the rest of the spies scrambled for their weapons. "We need to get out of here!"

Everyone rushed to the door, and Casey brought up the rear, placing a remote detonated bomb on the wall before heading out after the rest of them.

As they were racing down the hall, Chuck commented, "We need to get as far away from here as possible before any of their buddies come to provide back up. Our van won't be able to do that."

"Not since we ran into this little hiccup," Sarah added.

"You can fly out to our base with us," Coulson offered. "But we'll need your van to get to our jet."

Chuck nodded as he tried to see if his com was working. "That'll work since I still can't get ahold of Morgan."

"Who's Morgan?"

"The last member of our group," Chuck answered as they burst through the outside door and dashed towards their van.

Casey swung open the driver's door while Skye jumped into the passenger seat, and the rest of the group climbed in through the back. Morgan swiveled towards them in his chair. "Oh good, you're okay! I didn't know what to do when the coms went down… who are they?"

Chuck shook his head. "Never mind about that now, buddy," he answered as Casey floored it to the open field where the quinjet was sitting.

"Didn't know what to do when the coms went down?" Skye echoed. "How did you make it _this_ far into this kind of work? You sound worse off than FitzSimmons were when they first entered the field."

Casey shook his head. "Believe me; you don't want an answer to that question."

"Aw, come on, Casey. You know you love me!" Morgan commented, to which Casey responded with a low, annoyed growl.

OoOoO

"Despite the minor hiccups," Beckman began as she eyed Coulson and Gonzales standing with Chuck, Sarah, and Casey, "I want to congratulate you all for completing this mission. With the base in Minsk destroyed, along with all the intel on the device, this should mean no other organization will be developing _it_ from now on."

Coulson stepped towards the monitor the General was on, "Excuse me, ma'am, but would it be possible to know what kind of computer that was? Our computer specialist was only able to determine that it could hold an incredible amount of data."

Beckman took off her glasses and folded them in front of her. "I'm afraid I can't answer this. While this, unavoidably, turned into a joint op, this information must remain classified in order –"

"General," Gonzales interrupted, "it appears that they can't do their jobs to keep this – computer – safe; clearly people keep getting their hands on it. This classified computer should be given to an organization that will be able to keep it safe."

Beckman opened her mouth to answer, but Chuck raised a hand, indicating for her to stop. "General, if I may," he began, to which Beckman nodded. "What gives you the right to say that? S.H.I.E.L.D. fell because Hydra infiltrated the organization how many decades ago? They took how many dangerous weapons out of your possession? This computer, it has the potential to do a lot of good, as does most of the technology does today. However, there are people out there who will use technology to their benefit. That's what we've been fighting against – because people want to use this piece of technology for their own benefit, and not what it was originally designed for. The Ring infiltrated the CIA and the NSA years ago, and tried to use this technology for their advantage. While you may be rebuilding S.H.I.E.L.D., I can tell there's a divide here, so I don't know who to trust besides _my_ team," he said, gesturing between Gonzales and Coulson. "I don't want this computer to be used wrongly again."

"But why you?" Gonzales growled. "Why do you get to put the lid on it?"

"Because it's what my father would have wanted. He designed it."

After a tense silent moment between the two men, Beckman spoke up, "If that will be all, Mr. Gonzales, I would like to talk to my team. You and Coulson are dismissed."

The two S.H.I.E.L.D. agents left the room, but not without hesitation from Gonzales. Once the door closed, Beckman continued. "Were you able to download the data they had on their cypher?"

Sarah nodded. "Yes we did, General. We were able to successfully upload their files to one of Castle's servers."

"Good. Once you get back to Burbank, send any Hydra files they have to Coulson and his team. I'm sure it will prove useful."

"Understood," Casey replied.

"Now, to the more important question at hand… Chuck, do you know where to dispose of the Hydra Intersect components and their files on it?"

Chuck nodded his head. "Yes, General. I do."

"While Casey and Sarah send the files to S.H.I.E.L.D., I want you to dispose of it. Hopefully this will be the last we will ever hear of the Intersect," Beckman concluded before terminating the feed.

The three teammates exited the office. Sarah and Casey made their way to the hangar doors while Chuck hung back with Coulson. "Look, I just wanted to let you know that we'll be sending you all the Hydra intel that was on the computer within a few hours. Hopefully it will help with your fight against them."

"Thanks," Coulson trailed. "We appreciate that. Is there any chance you can tell me what the computer is? What it does?"

Chuck shook his head. "You don't want to know. It's too powerful a weapon for anyone to know about, let alone have. With any luck, those were the last people to know how to build it, or knew about it period outside of our team."

Coulson nodded. "Understood."

A few seconds later, Casey and Sarah approached them. "Have you seen Morgan?" Sarah asked.

The four agents all raised their eyebrows as they glanced at the area around them. "He was outside the door for the briefing," Chuck replied.

Before anyone could start to search for him, Morgan went running by the small group, saying at the top of his lungs, "This place is awesome!"

All three team members let out an agonized sigh as they rolled their eyes. "Because our base apparently isn't big enough for him… Casey, can you?" Chuck asked.

Casey growled in his response as he headed down the hallway to grab the little bearded man. "This isn't part of my job description…"

* * *

 _Epilogue_

Chuck pulled off of a small dirt road and onto a gravel driveway. Once he placed the car in park, he stepped out of the car and eyed the scenery. It was rare that he got a chance to see the woods like this. Not for a few years.

He shut the door behind him, went to the trunk, and pulled out the bag with all the information on the Intersect inside – any paper describing what it did or any spec on the smallest circuit board was shredded. All the built components were destroyed. Everything the enemy had on the Intersect was inside that bag.

After slinging it on his shoulder and grabbing the shovel he had brought, Chuck made his way into the woods. It didn't take him long to reach the spot that he recalled spotting one of the last times he was here – a rather large boulder. Chuck dropped the bag beside a nearby tree and proceeded to push the boulder out of the way. Several minutes later, Chuck grabbed the shovel and began digging. Once the hole was deep enough, he went over to the bag, grabbed it, and proceeded to bury it.

To make sure the dirt wouldn't settle and reveal the hiding place, Chuck packed the unearthed soil down as hard as he could before placing the boulder back in its original place. After he was finished, Chuck took a step back and wiped his brow. "There," he said as he was trying to catch his breath. "Now, let's hope it will stay buried in the past where it belongs," he declared just before he went back to his car.

As Chuck was pulling away, a figure immerged from the shadows and watched the car back out. A smile spread across the figure's lips once the car sped down the dirt road. "Aces, Charles. You're aces."

 _ **A/N: Hope you enjoyed it! Thank you to all that read, reviewed, favorited, and followed!**_


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